MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Reads0
Chats0
TLDR
A simplified scoring system is proposed that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length.Abstract:
A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homologous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.read more
Citations
More filters
Journal ArticleDOI
From benchtop to desktop: important considerations when designing amplicon sequencing workflows.
TL;DR: This paper focuses on aspects pertaining to the benchtop within typical amplicon workflows: sample screening, the target region, and library generation, and the impact of various data analysis parameters is investigated.
Journal ArticleDOI
Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains.
Nicholas R. Polato,Brian A. Gill,Alisha A. Shah,Miranda M. Gray,Kayce L. Casner,Antoine Barthelet,Philipp W. Messer,Mark P. Simmons,Juan M. Guayasamin,Andrea C. Encalada,Boris C. Kondratieff,Alexander S. Flecker,Steven A. Thomas,Cameron K. Ghalambor,N. LeRoy Poff,N. LeRoy Poff,W. Chris Funk,Kelly R. Zamudio +17 more
TL;DR: It is shown that tropical and temperate montane stream insects have diverged in thermal tolerance and dispersal capacity, two key traits that are drivers of isolation in montane populations.
Posted ContentDOI
Massive expansion of human gut bacteriophage diversity
Luis F. Camarillo-Guerrero,Alexandre Almeida,Alexandre Almeida,Guillermo Rangel-Pineros,Robert D. Finn,Trevor D. Lawley +5 more
TL;DR: The Gut Phage Database (GPD) is introduced, a collection of ∼142,000 non-redundant viral genomes obtained by mining a dataset of 28,060 globally distributed human gut metagenomes and 2,898 reference genomes of cultured gut bacteria to enable ecological and evolutionary analysis of human gut bacteriophages.
Journal ArticleDOI
The many faces of sequence alignment
TL;DR: This short review aims to summarise the current status of research in alignments, emphasising large-scale genomic comparisons and suggesting possible directions that will be explored in the near future.
Journal ArticleDOI
Crystal structure and computational characterization of the lytic polysaccharide monooxygenase GH61D from the basidiomycota fungus Phanerochaete chrysosporium
Miao Wu,Gregg T. Beckham,Gregg T. Beckham,Anna M. Larsson,Takuya Ishida,Seonah Kim,Christina M. Payne,Christina M. Payne,Michael E. Himmel,Michael F. Crowley,Svein Jarle Horn,Bjørge Westereng,Kiyohiko Igarashi,Masahiro Samejima,Jerry Ståhlberg,Vincent G. H. Eijsink,Mats Sandgren +16 more
TL;DR: The three-dimensional crystal structure of the basidiomycete Phanerochaete chrysosporium GH61D LPMO reveals a copper-bound active site common to LPMOs, a collection of aromatic and polar residues near the binding surface that may be responsible for regio-selectivity, and substantial differences in loop structures compared with other L PMO structures.
References
More filters
Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Journal ArticleDOI
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
TL;DR: Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
Book
Numerical Recipes in C: The Art of Scientific Computing
TL;DR: Numerical Recipes: The Art of Scientific Computing as discussed by the authors is a complete text and reference book on scientific computing with over 100 new routines (now well over 300 in all), plus upgraded versions of many of the original routines, with many new topics presented at the same accessible level.
Journal ArticleDOI
Improved tools for biological sequence comparison.
TL;DR: Three computer programs for comparisons of protein and DNA sequences can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity.